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- PDB-6u0a: Human Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Glycerol -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u0a | ||||||
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Title | Human Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) with Glycerol | ||||||
![]() | Angiopoietin-related protein 4 | ||||||
![]() | SIGNALING PROTEIN / Fibrinogen-like domain / Angiogenesis / Cancer cells / Metastasis | ||||||
Function / homology | ![]() negative regulation of lipoprotein lipase activity / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / endothelial cell apoptotic process / triglyceride homeostasis / enzyme inhibitor activity / protein unfolding / negative regulation of endothelial cell apoptotic process / lipid metabolic process / PPARA activates gene expression ...negative regulation of lipoprotein lipase activity / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / endothelial cell apoptotic process / triglyceride homeostasis / enzyme inhibitor activity / protein unfolding / negative regulation of endothelial cell apoptotic process / lipid metabolic process / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / positive regulation of angiogenesis / angiogenesis / collagen-containing extracellular matrix / blood microparticle / response to hypoxia / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Angiopoietin-Like 4 C-Terminal Domain (cANGPTL4) Reveal a Binding Pocket with Multiple Ligands Authors: Tarver, C.L. / Yuan, Q. / Singhal, A.J. / Ramaker, R. / Cooper, S. / Pusey, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 260.6 KB | Display | ![]() |
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Full document | ![]() | 260.5 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u1uC ![]() 1z3sS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24458.404 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain, residues 185-400 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ANGPTL4, ARP4, HFARP, PGAR, PP1158, PSEC0166, UNQ171/PRO197 Plasmid: pET3a / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.1 M HEPES 7.5, 0.1 M sodium chloride, and 1.6 M ammonium sulfate This solution with 20% glycerol was used as a cryoprotectant PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→47.44 Å / Num. obs: 20254 / % possible obs: 98.31 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.31 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.11→2.15 Å / Redundancy: 6 % / Rmerge(I) obs: 0.639 / Num. unique obs: 922 / CC1/2: 0.827 / Rpim(I) all: 0.28 / Rrim(I) all: 0.7 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Z3S Resolution: 2.11→47.16 Å / SU ML: 0.2073 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.9253
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→47.16 Å
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Refine LS restraints |
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LS refinement shell |
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